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Author SHA1 Message Date
Oliver Beckstein
02a0cbd58b link to the propka3 command page 2020-06-19 22:04:05 -07:00
Oliver Beckstein
fe70dc491a add sphinx deps to requirements.txt 
- sphinx
- sphinx_rtd_theme
 2020-06-19 21:38:45 -07:00
Oliver Beckstein
1c343a7d96 basic usage for propka3 command 2020-06-19 21:38:45 -07:00
Oliver Beckstein
59a97680d8 make ghpages to push to gh-pages branch 
- `make ghpages` will build the docs in docs/build/html and push it to an
  existing gh-pages branch; especially useful when building on a fork;
  you will have to initialize your gh-pages branch manually and enable
  docs on the gh-pages branch in the repo settings
- ignore build directories (top level build and docs/build)
 2020-06-19 21:38:39 -07:00
Oliver Beckstein
26a5ab042e API docs for propka 
- use autosummary (with custom module template)
- updated module docs for all modules so that they are included
  with sphinx autodocs
 2020-06-19 16:25:24 -07:00
Oliver Beckstein
65856b39fb use autosummary to generate most of the API Reference 
- custom _template/autosummary/module.rst to include docs
  for all module :members" (shows up directly after the summary
  tables)
- module docs should *not* contain autodocs for members, only general
  descriptions and examples
- all files inside api/ are autogenerated whenever sphinx is run
  (no need to add to the repository, hence excluded in .gitignore)
 2020-06-19 15:18:04 -07:00
Oliver Beckstein
2bf031fd65 initial sphinx docs 
starts #69

- basic structure
- RTD theme
- installation
- quickstart (more to do)
- references
- added start page with license and links to repo and issues
- authors in docs: papers and repo contributors (to be discussed)
 2020-06-19 12:13:53 -07:00
Nathan Baker
4875d9ee65 Merge pull request #61 from Electrostatics/nathan/v3.2 
Merge changes needed to release v3.2
 2020-06-19 07:37:49 -07:00
Nathan Baker
11bc32e9fc Require Python 3.6+. 
Fixes https://github.com/jensengroup/propka-3.1/pull/61#issuecomment-646190977
 2020-06-19 07:21:05 -07:00
Nathan Baker
77286be67a Add Microsoft Windows to OS list. 
Addresses https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442365647
 2020-06-19 06:52:06 -07:00
Nathan Baker
fb38d28f51 Add specific python versions to setup.py 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-06-19 06:46:36 -07:00
Nathan Baker
2f47d0ea9a Remove redundant PROPKA script. 
Fixes https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442401079
 2020-06-19 06:43:33 -07:00
Nathan Baker
9cd0da8ff3 Clean up README instructions. 
Remove references to setuptools and add some additional fixes.

Addresses https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442357797
 2020-06-19 06:39:07 -07:00
Nathan Baker
73e956f141 Add description of PROPKA versions. 
Implements suggestion https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442352878
 2020-06-19 06:28:01 -07:00
Nathan Baker
6b9f01a7c3 Standardize version references to "PROPKA 3". 
Partially addresses https://github.com/jensengroup/propka-3.1/pull/61#pullrequestreview-433445231
 2020-06-19 06:24:40 -07:00
Nathan Baker
c2ac407a96 Merge pull request #65 from jensengroup/read_parameter_file-KeyError 
Handle KeyError in read_parameter_file
 2020-06-19 05:48:09 -07:00
Thomas Holder
e80473db33 Handle KeyError in read_parameter_file 
Fixes basic usage of propka after `python setup.py install` followed by
`propka3 1ubq.pdb`
 2020-06-18 20:19:10 +02:00
Nathan Baker
18368b456a Remove setuptools discussion 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-06-18 09:53:51 -07:00
Nathan Baker
75057fbfef Remove specific version number 
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
 2020-06-18 09:53:17 -07:00
Nathan Baker
7a25ec6598 Update executable script name. 
Changed script name to propka3 based on https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442326049

Updated additional information in setup.py
 2020-06-18 08:57:12 -07:00
Nathan Baker
573b38db38 Fix stray propka31 to propka32. 2020-06-18 08:24:51 -07:00
Nathan Baker
a2196cdc6f Consolidate documentation. 
Addresses https://github.com/jensengroup/propka-3.1/pull/61#discussion_r442016279.
 2020-06-18 08:19:22 -07:00
Nathan Baker
2909173caf Add missing *.json to package data list. 2020-06-17 15:31:16 -07:00
Nathan Baker
0c4979560d Change propka31 to propka32. 2020-06-17 15:25:50 -07:00
Nathan Baker
4e7a41730d Change module version number. 2020-06-17 15:25:23 -07:00
Nathan Baker
0e4f565c90 Remove version number from tests. 
Tests aren't version-dependent.
 2020-06-17 15:24:20 -07:00
Nathan Baker
d52620d4e9 Update PROPKA header banner. 2020-06-17 15:24:00 -07:00
Nathan Baker
54294684b0 Remove broken links from README.md. 2020-06-17 13:22:17 -07:00
Nathan Baker
89a9eb15d4 Update INSTALL with better instructions. 
Remove explicit references to version 3.1 except for name of `propka31`
script which will be changed in subsequent commit.
 2020-06-17 13:17:33 -07:00
Nathan Baker
e8576fb4f3 Remove specific 3.1 version information. 
Except for name of script `propka31`; will handle that in another commit.
 2020-06-17 13:12:09 -07:00
Nathan Baker
1d8fa2bbbe Update setup.py with 3.2.0 information. 2020-06-17 12:33:52 -07:00
Nathan Baker
616540ebd6 Merge branch 'nathan/tempfile' 2020-06-03 18:36:47 -07:00
Nathan Baker
0cb470fbdb Merge pull request #59 from Electrostatics/nathan/tempfile 
Make PROPKA input file generation optional
 2020-06-03 18:36:27 -07:00
Nathan Baker
9126e3059f Fix PROPKA output naming. 
Addresses https://github.com/jensengroup/propka-3.1/pull/59#discussion_r434360267
 2020-06-03 18:34:12 -07:00
Nathan Baker
5d8e271420 Merge branch 'nathan/import' into nathan/tempfile 2020-06-03 17:51:16 -07:00
Nathan Baker
879c48a3d8 Merge branch 'nathan/import' 2020-06-03 17:50:56 -07:00
Nathan Baker
df028e445b Merge pull request #50 from Electrostatics/nathan/import 
Resolve cyclic import issues
 2020-06-03 17:50:30 -07:00
Nathan Baker
7085271ad5 Simplify with .writable() method. 
Addresses https://github.com/jensengroup/propka-3.1/pull/50#discussion_r434349737
 2020-06-03 17:49:19 -07:00
Nathan Baker
9b59d924b2 Make PROPKA input file generation optional. 
Fixes https://github.com/jensengroup/propka-3.1/issues/51.
 2020-05-31 10:26:56 -07:00
Nathan Baker
1d17cb05ed Remove TODO for refactoring. 
Done already.
 2020-05-30 13:15:45 -07:00
Nathan Baker
52554d905a Remove TODO statements for refactoring. 
Already done.
 2020-05-30 13:12:44 -07:00
Nathan Baker
84846aad8c Resolve cyclic import problem. 
Fixes https://github.com/jensengroup/propka-3.1/issues/49

Moved I/O into higher level of of code; should make
issue https://github.com/jensengroup/propka-3.1/issues/51
easier to resolve
 2020-05-30 12:01:30 -07:00
Nathan Baker
b597a6f257 Remove cyclic import based on I/O in pdb.py. 
Partially addresses https://github.com/jensengroup/propka-3.1/issues/49
 2020-05-30 10:00:31 -07:00
Nathan Baker
397d5e10aa Remove cyclic import based on atom.py 
Partially addresses https://github.com/jensengroup/propka-3.1/issues/49
 2020-05-30 09:26:13 -07:00
Nathan Baker
461edda3b2 Break propka.calculations into parts. 
Broken into three files to simplify import analysis:

* `calculations.py` - distance calculations and simple math
* `energy.py` - energy calculations
* `hydrogens.py` - hydrogen geometry calculations

Working towards addressing https://github.com/jensengroup/propka-3.1/issues/49
 2020-05-30 08:45:39 -07:00
Nathan Baker
dde0d67ea5 Merge pull request #40 from Electrostatics/nathan/delint 
De-lint PROPKA
 2020-05-30 08:14:45 -07:00
Nathan Baker
d7147799d8 Python formatting is annoying. 
I sometimes miss C -- but only with output formatting.  C++ cout marks
some decline of civilization, I think...

Addresses https://github.com/jensengroup/propka-3.1/pull/40#discussion_r432313434
 2020-05-29 20:55:32 -07:00
Nathan Baker
a716c89a36 Remove unused argument from Atom() constructor. 2020-05-29 20:49:47 -07:00
Nathan Baker
5010d9fa14 Merge branch 'nathan/strings' into nathan/delint 2020-05-29 20:41:53 -07:00
Nathan Baker
83a7099d79 Fix my formatting mistakes. 
Python formatting makes me miss K&R C.
 2020-05-29 20:37:47 -07:00